


A New James Kirk

by catsinthetardis



Series: Always-an-Augment-Kirk [1]
Category: Star Trek: Alternate Original Series (Movies)
Genre: M/M, george kirk was secretly an augment
Language: English
Status: Completed
Published: 2014-08-04
Updated: 2014-09-29
Packaged: 2018-02-11 17:06:17
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 5
Words: 9,120
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2076087
Author URL: https://archiveofourown.org/users/catsinthetardis/pseuds/catsinthetardis
Summary: <blockquote class="userstuff">
              <p>What if George Kirk had been an augment? How would that change the Into Darkness storyline?<br/>*previously James Kirk's Messed Up Family</p>
            </blockquote>





	1. Discovery

Khan discovered in the fourth month of his imprisonment and forced servitude that he was not the first augment to have been awakened. Understandably, he was furious. He resolved to find out the identity of the other augment, and two months later, unearthed the classified _Narada_ files. 

Previously, he had been under the presumption that his people had been found after this incident, but he was forced to reconsider after finding the crew profiles. George Kirk looked exactly like Otto, and it was unsurprising that he had taken charge at the pivotal moment of the conflict. However, Khan was puzzled for a moment about the suicidal charge against the _Narada_. It went against every instinct an augment possessed, but it made sense when Khan found the "Survived By" column and saw "Son: James Tiberius Kirk." Shock hit Khan like one of the many phaser blasts Marcus' cronies had fired at him. Evidently, Marcus wasn't the only Starfleet officer who had loose morals and did not object to manipulation.

Khan suspected that the only reason James had been born was that Earth couldn't keep track of every moment in every ship.  
It had actually been quite clever of Otto to force Starfleet to protect him by eloping with a Starfleet member. And this had rubbed Starfleet officials the wrong way, ensuring a coverup and the unwillingness to risk waking other augments. 

Khan had no doubt that Marcus truly thought the _Botany Bay_ had been found after the _Narada_ incident and did not know the true history of George Kirk, but this sparked the question of who knew the truth. 

Reading the rest of the file, Khan was overwhelmed by pride in James, who had saved his own crew and was now captain of the flagship of the Federation. The _Enterprise_ was a marvel to be envied. 

Khan was also intrigued by the mentions of Christopher Pike. In his own experience, Pike had no knowledge of Section 31 or any of Marcus' plots. After reading Kirk's file, however, Pike seemed to be less a benevolent paternal figure and more shadow player. 

Khan couldn't be sure of the endgame, but as anything to do with his people, he feared the worst. Kirk's file was worrying to Khan. Its classified status wasn't surprising to one who knew his true history, but it appeared that wasn't the only reason. 

The levels of incompetency and madness that was the mess of Tarsus IV stunned even Khan. It seemed that James had already had his fair share of trouble and danger, as well as a protective instinct. Kodos had a lot to answer for. 

However, any plans to hunt Kodos down had to be put on the back burner, pending the safety and revival of the rest of Khan's crew. Knowing his privacy was coming to an end, Khan expunged any records or evidence of his snooping and placed the padd back in the ensign’s bag, where it had been so conveniently located.


	2. Lost and Found

**Summary for the Chapter:**

> just moving through the movie's story, ends on Kronos

**Notes for the Chapter:**

> *not beta read* read at own risk! if there are any horrible errors please let me know, i'll fix them

*Six months later*

How had everything gone to hell so quickly? Khan had been so close to securing the safety of his people by hiding the cryotubes in the torpedoes. Unfortunately, his last trip into the storage area had been discovered somehow. Marcus had most likely disposed of his remaining crew by now.

Anger, sheer rage, was the only emotion Khan was currently capable of, but it didn’t stop him from formulating a plan of revenge.

Khan left for the Royal Children’s Hospital, where Thomas Harewood’s daughter was suffering from a disease that would soon kill her. Knowing of Harewood’s proclivity to visit before his shift, and his access to the archives, Khan grabbed a coat that would cover his Starfleet shirt and waited.

As soon as Khan saw Harewood, he moved outside of his daughter’s room and watched until Harewood emerged.

“I can save her.”

The Starfleet officer had been remarkably easy to convince, and Khan had no doubt he’d send a message to Marcus, but that no longer mattered because that man no longer had any hold on him. The promise of saving his family was enough to motivate Harewood into blowing up a public space, and Khan would have been surprised if he hadn’t organized the whole charade for his own.

Otto would have laughed at the irony of his monument being instrumental in avenging his larger family.

During Harewood’s lunch break, Khan smuggled the canister that contained the serum and the explosive device disguised as Harewood’s Starfleet Academy ring into his bag as he was leaving the archive. Khan discreetly shadowed him and watched his relief as the vital signs of his daughter began creeping towards normal. Eyes inexplicably burning, Khan left the hospital to watch the fireworks.

Taking so much time to learn the new technology and weaponry was paying off as Khan uploaded a program into the jumpship’s targeting system. There was no doubt James would be at Daystrom, as all captains were required to attend emergency meetings, as the act of blowing up a public archive would surely qualify as.

Piloting the jumpship to San Francisco would take remainder of the day, so Khan modified the traswarp device to make it capable of transporting large objects. He had studied the layout of San Francisco, and was confident that he wouldn’t simply crash into a building. For an augment, that would simply be embarrassing.

San Francisco was eight hours behind London in terms of time zone, but the news of the Kelvin Memorial Archives would reach Starfleet Headquarters almost instantaneously.

He would be prepared to defend himself on Kronos until Marcus came to get him. A war between the Federation and the Klingons would not be beneficial at this stage, but the chaos would buy Khan time to perfect his plans.

Khan appeared in San Francisco with London Starfleet jumpship 208 just as the sun was setting and night began. Earlier, he had changed into more appropriate clothing for his approaching trip to Kronos.

Khan had spent months formulating a plan for his revenge, but nothing could have prepared him for the beautiful sight of Marcus’ comprehension as the jumpship came into view of Daystrom. It seemed Khan had been figured out, judging by James’ stance and lack of surprise on his face as he turned and yelled.

“Clear the room!”

However, James seemed to be the only person who had followed Khan’s train of thought, and the lack of the Captain insignia registered to Khan an instant before he opened fire.

A snarl twisted Khan’s face as he destroyed the conference room. There was no satisfaction to be had for Khan, this was simply too easy. Starfleet was so predictable and slow to react, it should have been impossible for such plebeians to destroy the last members of his crew. Khan watched as James ran out of the room into the hallway, and wondered at Kirk’s actions.

Kirk’s intent became clear a moment later as the small ship began taking fire from a phaser rifle. The futility of the act was quickly noticed by Kirk, and the fire stopped. Khan turned his attention back to the room, and watched for Marcus. Unfortunately, his body could not be seen, and Khan was forced to accept that Marcus would most likely survive his attack.

Suddenly, there was a shattering noise, and the jumpship’s intake whined alarmingly before the ship began shaking violently and dropping in altitude. 

Khan locked eyes with Kirk and grinned savagely at him before activating the transwarp device. As the golden beams surrounded him, Khan saw Kirk’s features distorted by a scowl.

Kronos was a ghost world, almost completely abandoned by the Klingon Empire. As soon as he materialized, Khan pulled his hood up and ran for a building. It would do him no good to be seen just yet, as Klingons were hostile to every other species. Earlier in the year, Khan had sent weapons and other supplies ahead to Kronos in case of an emergency such as this.

After finding his supplies, Khan would have to wait for Marcus or some poor peon he would send as a sacrifice to start a war. If Marcus had killed his crew, Kirk would soon be the only remnant of the once mighty race. It was likely that Kirk had no idea he was half augment, and unless Khan had a chance of taking Kirk far away from Starfleet, he never would.

Time passed slowly for Khan as he waited for his judge, jury and executioner. There was nothing to do in the Ketha district, as it had been deserted decades ago. Khan continued to streamline and modify the weapons sent here months ago and visualize how he would best like to kill Marcus.

Almost two days passed before Khan heard anything from Starfleet. Klingon activity in the sector was increasing, and the risk of being found by them increased greatly. During one of the breaks in patrol, Khan was suddenly assaulted by noise.

_'Attention, John Harrison.'_

Evidently, Marcus had not released his true identity. But if this ship was taking the time to announce their presence, there was a chance of him being able to come aboard and get back to Earth and finish what he started.

 _'This is Captain Hikaru Sulu of the USS Enterprise_.'

Was Kirk not Captain? Khan was sure he’d killed Pike, and James had been the apparent First Officer. There was something afoot.

_'A shuttle of highly trained officers is on its way to your location.'_

Khan snorted. Any team of “highly trained officers” would be unlikely to even get close to him unless it was comprised entirely of Vulcans. And as Vulcans were pacifists and there was only one in Starfleet, the chance was slim to none. One of his options would be to kill the team, commandeer the shuttle, and return to the ship it came from, but the _Enterprise_ would simply blow him out of the sky.

_'If you do not surrender to them immediately, I will launch the entire payload of advanced long range torpedoes, currently locked onto your location.'_

The rest of the message was lost to Khan as thoughts whirled around in his head. His crew was alive! There was a chance to retrieve his crew now. Kirk could come later, as evidently he was no longer serving aboard the _Enterprise_. With his crew, Khan would be unstoppable.

_'...If you test me, you will fail.'_

This Hikaru Sulu was excellent at bluffing. If Khan had been a normal human, he would have no doubt he would surrender. Unfortunately for this Sulu, Khan was not a normal human. The first order of business in Khan’s emerging plan was to confirm all the torpedoes were present. Marcus had no doubt ordered Khan’s immediate destruction, and would not have removed Khan’s crew from the torpedoes.

Marcus had made his first mistake. Assuming everyone else in Starfleet was as bloodthirsty as he was a fatal error. In an exploration and science-based organization, Khan now had the pleasure of meeting the less militaristic side.

Lights from a Klingon ship’s guns began flashing in the distance, and Khan ran towards the edge of the building he was standing on. An explosion rocked the foundations, and a small Knormian ship came flying out of a fissure between two buildings that had collapsed against each other. Khan backed up and prepared to save their lives from the Klingons that were in all probability waiting further up.

The suddenness and multitude of the floodlights that turned on as the ship coasted to a stop surprised Khan for a brief moment. A solitary figure emerged from the grounded ship to approach the group of burly Klingons. Khan watched as the lone person began talking to the group. Evidently, they said something wrong, and the leader of the Klingons’ hand shot up and grabbed their face. The other hand drifted to where Khan knew a knife would be holstered.

Well, if Khan allowed this human to die he would lose the trust of the crew.

Khan opened fire with the blaster, and watched with satisfaction as the lower area descended into chaos. The human who had been dropped by the Klingon grabbed the knife from his own holster and drove it into his groin area. Four more humans emerged from the Knormian ship and joined the melee. A ship pulled around to open fire on Khan, but he hefted his larger cannon and pumped a stream of energy into the main cabin. Keening, it spun away and exploded.

Two of the humans were slain by Klingons, but Khan had no time to watch as he attempted to find the remaining three while waves of Klingons assaulted him on the platform. One was barely fending off the third Klingon that had snuck up behind him. Khan turned away briefly, and when he looked back there was a Klingon smashing the man’s head with a rifle butt. 

Turning the cannon on the scene, Khan opened fire and half a Klingon fell away from the only crewmember he had seen. The man was found by the two others, and was dragged behind a partition.

Once all the crewmembers were out of his way, Khan turned his full attention to the Klingons and decimated them. Taking a running start, Khan cast aside the cannon and leaped off the platform toward where he had last seen the three people. His hand-to-hand had been neglected as late, but Khan managed with the knives he had scavenged. Making his way towards the trio, one pointed a Klingon rifle at him. Ignoring the weapon, Khan stared down the injured man.

“Stand down!”

To his surprise, it appeared to be Kirk. Khan was near the end of his patience, the Klingons had been annoyingly numerous and the now identified Vulcan was being persistent.

“How many torpedoes?” 

“Stand down!”

Losing his mind with worry, Khan shot the rifle out of the Vulcan’s hands.

“Your torpedoes! The weapons you threatened me with in your message. How many are there?”

For a tense moment, no one answered his question and Khan began to doubt if his crew had really survived. Then, the Vulcan answered from his side.

“Seventy-two.”

Relief coursed through Khan, and he paused a moment to savor the moment. Then he dropped his weapon.

“I surrender.”

Kirk, who had been silent so far, stood and addressed him.

“On behalf of Christopher Pike, my friend, I accept your surrender.”

Suddenly, Kirk spun around and began pummeling Khan. The strength of the hits was surprising, considering the beating he had taken at the hands of the Klingons, but there was nothing to suggest that Kirk was anything but normal. Khan let his mouth curl into a small smirk as the female screamed at Kirk.

“Captain!”

Turning his head, Khan looked up at the breathless Kirk.

_“Captain.”_

**Notes for the Chapter:**

> yeah, not much deviating from Into Darkness. really, there won't be much deviation until the end. it's more of a ua than au
> 
> *so i fixed a couple things to make it more coherent, and i discovered things weren't italicizing automatically so i fixed that  
> the third chapter should be up really soon


	3. Chapter 3

**Notes for the Chapter:**

> yeah, sorry for the delay

The march through the _Enterprise_ was dull, and Khan kept up his expression of boredom throughout. He was placed in a cell that was reminiscent of movies from his era where the villain was placed in a large glass cage. Evidently, Starfleet designers had seen the _Avengers_ one too many times.

In a manner that suggested he was a king waiting for his attendants, Khan stood in the holding cell. Kirk walked in, flanked by two officers, both wearing blue shirts. The Vulcan and Kirk had changed out of their costumes quickly.

The remaining officer walked up to the partition and pulled the small metal opening over, enlarging it in the process.

“Put your arm through the hole, I’m going to take a blood sample.”

Khan complied, rolling up his sleeve and turning to face Kirk as he stuck his arm through the opening. Not having felt the thrum of a moving ship, Khan began to needle Kirk.

“Why aren’t we moving? Surely there hasn’t been a mechanical failure. Perhaps in your warp core? How inconvenient that it places you dead on the edge of the neutral zone.”

Openly shocked, the medical officer looked up. To his credit, the syringe didn’t move an inch. He had remarkably steady hands.

“How the hell would you know that?”

Kirk turned his head sharply towards the doctor.

“Bones.”

Smirking slightly, Khan continued.

“I think you would find my information valuable, Captain.”

As Kirk stared him down, “Bones” withdrew the syringe. Kirk turned back to his crewmember.

“Are we good?”

“Yeah.”

Kirk turned to leave with his entourage.

“If you will not listen, you will be responsible for the death of your entire crew and family.”

Pausing, Kirk turned his step into an about-face and stalked closer.

Khan could almost hear the sighs of exasperation from his crewmates.

“Let me explain something. You are a criminal. You are only alive right now because I allowed it. I was authorized to _end_ you on Kronos.”

“So why did you allow me to live?”

This obviously struck a chord with Kirk. He shifted on his feet a brief moment before replying.

“We all make mistakes.”

Glancing down, Khan smirked. Kirk didn’t know it, but there was another reason. While Khan would undoubtedly be dead if Kirk’s crew had not convinced him to alter his actions, now that they had met face-to-face there would be a subconscious battle regarding decisions related to Khan. Augments had been engineered to follow a leader to minimize in-house fighting, and while Kirk was the only part-augment, there had been no previous challenger to his authority.

“Oh, Captain. I surrendered to you on Kronos because despite your best efforts to prove otherwise, I think you have a conscience. If you did not, I would already be dead, and you would be incapable of hearing the truth. 23, 17, 46, 11. Coordinates not far from Earth. If you want to know why I did what I did, go take a look.”

“Why should I listen to you? Give me one good reason.”

“I can give you 72. And they’re all aboard this ship. They have been all along. I suggest you open one.”

Of course, only 71 were in torpedoes. Kirk left, and Khan settled in for the imminent boredom that would soon follow. Khan fervently hoped that they would not open the empty one by mistake.


	4. Chapter 4

“Why is there a man in that torpedo?”

Kirk had met his challenge sooner than he had anticipated. That was fortunate. Khan turned his head to Kirk.

“There are men and women in all those torpedoes Captain. I put them there.”

“Who the hell are you.”

It was not a question. It was a suspicion confirmed that Khan was not who the record said he was.

“A remnant of a time long past. Genetically engineered to be superior so as to lead others to peace in a world at war. We were condemned as criminals, forced into exile. For centuries we slept, hoping that when we awoke things would be better.” 

Khan stared at the Vulcan present, making up a story in front of a being who was excellent at detecting lies.

“But as a result of the destruction of Vulcan, your Starfleet began aggressively searching distant quadrants of space. My ship was found adrift, and I alone was awakened.”

“I looked up John Harrison. Until a year ago, he didn’t exist.”

And here was the reveal.

Raising his voice, Khan almost yelled at Kirk. To complete the illusion of outrage, Khan rose from the bench he had been sitting on and moved towards Kirk.

“John Harrison was a fiction. Created by your Admiral Marcus, a smokescreen to conceal my true identity. My name is Khan.”

If Kirk understood the repercussions of the statement he gave no indication. The Vulcan, too, did not react.

“Why would a Starfleet admiral ask a 300-year old frozen man for help?”

“Because I am better.”

“At what?”

“Everything.”

“Alexander Marcus needed to respond to an uncivilized threat in a civilized time. And for that, he needed a warrior’s mind. My mind. To design weapons and warships.”

This interrogation was going incredibly slowly. Khan paced in the cell, both for appearance and actual nerves. Soon, Marcus would be here, and he needed Kirk to at least recognize that Marcus could not be defeated without him.

The Vulcan, silent until this point spoke up.

“You are suggesting that the Admiral violated every regulation he vowed to uphold, simply because he wanted to exploit your intellect.”

Almost snarling, Khan rounded on the impertinent Vulcan.

“He wanted to exploit my savagery. Intellect alone is useless in a fight. You. You can’t even break a rule. How can you be expected to break bone.”

If everything fell apart, it would be because of the Vulcan. Vulcans were pacifists, and were incapable of imagining the weapons that Khan had designed. That would presently be trained on them. Dismissing the Vulcan, Khan turned back to Kirk.

“Marcus used me to design weapons to help him realize his dream of a militarized Starfleet. He sent you to use those weapons. To fire my torpedoes on an unsuspecting planet.”

Kirk looked uncomfortable with the revelation that Marcus had set them up. His eyes shifted towards the Vulcan and back to Khan.

“And then he purposely crippled your ship in enemy space, leading to one inevitable outcome. The Klingons would come searching for whomever was responsible, and you would have no chance at escape. Marcus would finally have the war he always wanted.”

“No.”

Kirk moved closer to his First Officer.

“I watched you open fire on a room full of unarmed Starfleet Officers. You killed them, in cold blood.”

Despairingly, Khan shook his head at the floor.

“Marcus took my crew from me.”

“You are a murderer!”

Khan stalked away from the glass, turning his back. The best lies had an element of truth to them.

“He used my friends to _control_ me. I tried to smuggle them to safety in the very weapons I had designed. But I was discovered. I had no choice but to escape alone. And when I did, I had every reason to assume that Marcus had killed every single one of the people I hold most dear.”

Letting a single tear escape, Khan continued, turning back to the duo standing outside.

“So I responded in kind. My crew is my family.”

Watching Kirk carefully, Khan played his trump card.

“Is there anything you would not do for your family?”

In that moment, Kirk looked lost. Khan prepared to continue talking, but a harsh beep sounded and a voice from the ceiling spoke.

_‘Proximity alert, sir.’_

Kirk turned away, blinking like he was coming out of a trance. Khan cursed the timing of Marcus.

_‘There’s a ship at warp headed right for us.’_

“Klingons?”

Khan could see the gears in Kirk’s mind turning. Despite the recent revelation, Kirk was in denial about Admiral Marcus, but he knew who would be at warp, and it wasn’t Klingons. Khan decided to give his thought process a kick.

“At warp? No, Kirk. We both know who it is.”

The fragile hope in Kirk’s eyes died as the official response came from the bridge. 

_‘I don’t think so. It’s not coming at us from Kronos.’_

Kirk held Khan’s stare for a moment. Abruptly, Kirk turned and ran for the bridge.

“Lieutenant move Khan to medbay, post six security officers on him.”

As if such a paltry number would be capable of restraining him. But Khan would allow the illusion for now.


	5. Chapter 5

Khan was eagerly anticipating the inevitable trip to the Vengeance. Between the boredom of being confined to the brig and the nervousness he would not admit to, he was tightly wound. Marcus was undoubtedly attempting to pressure Kirk into revealing where he was, and Khan was uncertain of Kirk’s performance abilities when his own crew was at stake.

Fortunately, Kirk was savvy enough to move Khan to a safer location. Khan sat unnaturally still on the standard bed until Kirk walked in the room.

“I will do everything I can to make you pay for what you did. But right now, I need your help, because you obviously know something we don’t.”

Unable to resist testing the waters, Khan decided to reply.

“In exchange for what?”

“Currently, both of our crews are onboard this ship. Marcus is trying to blow it up. Don’t act like either of us have a choice right now.”

Evidently, when Kirk was worked up he had a sharp tongue. And he had learned from Marcus’ mistakes, not to use his crew as collateral. Kirk was distracted, however by the CMO, who was handling a small piece of fluff.

“Bones, what are you doing with that tribble?”

“Khan’s cells regenerate like nothing I’ve ever seen before. I’m injecting his platelets into this dead furball for science Jim.”

Khan brought the Captain’s attention back to the issue at hand.

“You are correct in your analysis, Captain. There is no other option than to disable the Vengeance if you wish to save your crew."

Kirk had listened to him, and now there was a chance to save the rest of his crew and kill Marcus. The flippancy of Kirk was surprising, given the near-impossible odds of their survival, but Khan supposed he was worried but wouldn’t concern his crew with his own doubts. Or expose weakness in front of a possible enemy. Kirk was an excellent leader, listening to his crew and making decisions that included their input if it would truly help. Which was fortunate, as without the crew’s input, Khan would most likely be dead in Klingon space along with the _Enterprise_ and her crew because of Marcus’ meddling.

Settling into a more optimal position in preparation for launch, Khan felt Kirk almost instantly follow suit.

Khan heard Kirk begin to talk to the crewmember that had snuck onboard the Vengeance.

“Scotty, how we doing over there?”

_‘Captain, I wish I had better news. They blocked our access to the ship’s computer. They’ll have full weapons in three minutes. That means next time I won’t be able to stop them destroying the Enterprise, standby.’_

The first officer’s voice crackled over the comm.

_‘Captain, the ships are aligned.’_

“Copy that. Scotty!”

_‘I’m running, standby.’_

Khan could hear panting on the comm from “Scotty” and almost laughed at the absurdity of Kirk’s crew. But this Scotty was obviously smart, weapons supposedly weren’t accessible off the bridge.

_‘Woah, woah, woah. I dunno, Captain. This door is very wee, I mean, you know, small. It’s four meters, tops. It’s gonna be like jumping out of a moving car, off a bridge, into a shot glass.’_

“It’s okay, I’ve done it before.”

Khan swiveled his head to look quizzically at Kirk. Just how many situations can be described as what they’re about to do? Kirk glanced at him and began to explain.

“Yeah, it was vertical. We jumped onto a…uh…it doesn’t matter. Scotty…”

The full story would have to be disclosed at a later time, but Khan suspected it had to do with the Nerada incident, perhaps the drill that was mentioned. For now, there were bigger problems, and Kirk needed to stay focused if he wished to survive. Distantly, Khan thought he remembered something important about the Nerada, but he shook the thought out to contemplate later.

“Did you find the manual override?”

Suddenly, Kirk blustered over Khan, “The manual override, Scotty?”

_‘Not yet! Not yet!’_

The sound of footsteps echoing in a large area was prevalent for a second more, and then stopped abruptly.

Acting Captain Spock’s voice once again interrupted.

_‘Captain, before you launch you should be aware that there is a considerable debris field between our ships.’_

“Spock, not now. Scotty, you good?”

_‘It’s not easy! Just give me two seconds, alright? You mad bastard! Come on, come on. Yes! Okay, okay. I’ve set it to open the door.’_

Kirk looked over at Khan again and asked “You ready?”

“Are you?”

Both turned back to the door separating them from space.

“Spock, pull the trigger.”

_‘Yes Captain. Launching activation sequence in three…two…one.’_

A sudden, harsh pull, and both Khan and Kirk were jettisoned into space. There could be no miscalculations now, or death would be the swift consequence.

_‘Captain, there is debris directly ahead.’_

_‘Copy that.’_

Khan watched Kirk veer away, sending himself off the course. He was still in an optimal position, but there was significant debris in the near distance. The chief medical officer’s voice sounded on the comm.

_‘Woah, Jim! You’re way off course!’_

_‘I know, I know! I can see that!’_

A different voice, the imposter Captain from Kronos, came to life.

_‘Use your display compass, Captain. You must correct precisely thirty-seven point two-four-three degrees.’_

_‘Got it. I’m working my way back. Scotty, you’re going to be ready with that door, right?’_

Only silence came from the other end, and Khan silently hoped that Marcus’ crew hadn’t killed him or he and Kirk would be smashed against the side of the Vengeance like bugs on the windshield of a car.

_‘Mr. Scott, where are you?’_

_‘Captain, he can’t seem to hear you. I’m working on getting his signal back, standby.’_

The communication officer seemed unsure of why Mr. Scott would not reply, and Khan again wished for the most likely scenario to be incorrect. At that moment, Khan heard a sharp noise from Kirk’s channel, but had no time to hear the conversation that ensued.

_‘Khan, use evasive action, there is debris directly ahead.’_

“I see it.”

Slabs of sharp metal careened by as Khan navigated the debris patch. The nature of the detritus was mechanical, and Khan watched as his radar blinked out. A thought suddenly occurred to him, about what he had seen in the Nerada report, and he hit a chunk of hull that had blended against the Vengeance in his shock. Khan fought to regain his positioning for further travel. Fortunately, the heads-up display began functioning again as well as the incoming comm signal as he set himself back on course. 

_‘Captain, you need to adjust your target destination to one-eight-three by four-seven-three degrees.’_

_‘Spock, my display is dead. I’m flying blind.’_

_‘Captain, without your display compass, hitting your target destination is mathematically impossible.’_

_‘Spock, if I get back, we really need to talk about your bedside manner.’_

Khan listened as Kirk told the bridge crew that his display was dead and watched his screen for the comm ready light. It flickered back to life as he exited that bit of debris, and he immediately began talking into the comm.

“My display is still functioning. I see you Kirk, you’re two hundred meters ahead at my one o’clock. Cut to your left a few degrees and follow me.”

If this was how Kirk’s missions always went, it was a wonder he was still alive.

_‘Scotty, we’re getting close. Do you copy?’_

Evidently contact was still out with Mr. Scott, and the door was approaching rapidly. There was a small amount of panic evident in Kirk’s voice, and Khan could not blame him. The divot in the hull was now visible to Khan, which made it about ten seconds out.

_‘Do you copy, Scotty?’_

Acting Captain Spock began counting down, and Khan admired the logic of the Vulcan covering all the possibilities. It also occurred to Khan that the Vulcan was cunning, and could work any situation to his advantage regardless of variables, despite his constant recitation of them.

_‘If you can hear us, Mr. Scott, open the door in ten, nine…’_

_‘Scotty!’_

_‘…eight, seven…’_

_‘Mr. Scott, where are you?’_

_‘…six…’_

An unknown voice also began counting down the distance between numbers.

_‘Eighteen hundred meters.’_

_‘…five, four…’_

_‘Sixteen hundred meters.’_

Commander Spock and Kirk’s voices became almost one and the same as they flew towards the door.

_‘Scotty, where are you?’_

_‘…three…’_

_‘Do you copy, Scotty? Please!’_

_‘…two… Mr. Scott, open the door.’_

_‘Open the door!’_

_‘Mr. Scott, now!’_

Only at the very last moment did the chute open, and only Khan noticed the body that flew out as he and Kirk entered. It seemed that this Mr. Scott had successfully distracted a crewmember long enough for him to let them in. Khan twisted himself and Kirk sideways to roll to a stop. As Kirk seemed to have at least some of an augment’s durability, or at least freakishly good luck regarding these stunts, Khan released Kirk to stop himself. 

They both ended up at the foot of the console, and Khan sat up and watched to make sure Kirk had not caused injury to himself. Really, Khan needed to kickstart the augment half of Kirk before he killed himself in these escapades. Kirk pushed himself to a kneeling position and groaned. The man who must be Mr. Scott, or “Scotty,” as Kirk called him, sat at the base of the console with his wrist tied to a strut.

“Welcome aboard.”

Kirk sat up with another groan, and stretched his back.

“It’s good to see you Scotty.”

Khan watched as Mr. Scott looked confusedly in his direction.

“Who is that?”

Gesturing between Mr. Scott and Khan, Kirk introduced them.

“Khan, Scotty, Scotty, Khan.”

Mr. Scott nodded politely.

“Hello.”

Khan stood up fully and walked to the console. Kirk followed, and Mr. Scott stood back up and untied his wrist.

“They’ll know we’re here. I know the best way to the bridge.”

Khan began stripping out of his suit along with Kirk, and Scotty stood nearby examining Kirk’s broken helmet muttering improvements under his breath. Kirk handed Khan a phaser, and Khan couldn’t quite mask his surprise.

“It’s locked to stun.”

Surprise turned to disappointment and disdain, and no visual cues of the small bit of respect. Khan appreciated that Kirk didn’t wish to kill fellow Starfleet members, but they were keeping his crew from him and protecting Marcus. There would be no mercy from him.

“Theirs won’t be.”

“Try not to get shot.”

Khan was amused by the response, but was too close to his goal to spare a moment for banter. His concern lay with Kirk, for phasers weren’t as effective against himself. Leading with his phaser, Khan began stalking further into the ship. A concern was voiced by Mr. Scott.

“They’re gonna have full power and we’re walking!”

It was a fair point, but other options were not viable. Khan paused at a console and tucked his phaser into his belt while answering,

“The turbo-lifts are easily tracked and Marcus would have us in a cage. This path takes us to the Engine room. They know they won’t be able to use their weapons here without destabilizing the warp core, which gives us the advantage.”

“Where’d you find this guy?”

“It’s a long story.”

The group continued to make their way to the bridge, and Mr. Scott continued to ask questions.

“I don’t mean to tempt fate here, but where is everybody?”

“The ship is designed to be controlled by minimal crew, one if necessary.”

“One?”

Khan nodded and noticed the security guard running towards him, violently subduing him. In his peripheral vision, he watched as Mr. Scott and Kirk backed up and became engaged by the rest of the patrol. He slipped away quietly to monitor them and ensure there were no stray officers.

Kirk fought viciously, with heavy swings and closed fists. His stance was optimal and provided a small target for aggressors while enabling movement. There was an obvious element of krav maga, as well as a more wild style that defied prediction. It seemed Kirk was quite capable of defending himself against normal humans. He took a hit, but stayed up and continued fighting. His guard went down hard, helped along by a blow to the back of their neck, and Kirk turned to help Mr. Scott.

“You alright?”

“Yeah.”

Mr. Scott noticed his absence first and pointed it out to Kirk.

“Where’s Khan?”

“Shit!”

Taking a brief moment to be amused, Khan stepped out of the row behind them and gestured along the path. 

“This way.”

He began walking away, but made sure to keep within earshot of the pair. Khan could be much farther away due to his superior hearing, and it appeared that Kirk had forgotten that.

“The minute we get to the bridge, drop him.”

“What, stun him? Khan? I thought he was helping us?”

“I’m pretty sure we’re helping him.”

Ah. Clever boy. Of course, now there would be a change of plans. Kirk was no longer exempt from small harm. As his group reached the bridge, Khan could hear the dialogue from the other side.

“Power coming online, sir.”

“Retarget the _Enterprise_ now.”

“Aye sir.”

Mr. Scott, Kirk, and himself burst onto the bridge, firing away with their phasers. Khan turned his back to Mr. Scott, pretending to do something on a console and waited briefly before feeling the sting of a stun. The force pushed him down, and he played dead so to speak, as Kirk and Mr. Scott took control of the bridge.

“Make sure he stays down.”

Khan had no intention of conceding to Mr. Scott, however, and waited for his opportunity. Listening carefully for his cue, he heard as Mr. Scott made his way over to him, passing Marcus’ daughter. After the footsteps ended, he heard Kirk begin to talk to Marcus.

“Admiral Marcus, you are under arrest.”

“You’re not actually going to do this, are you?”

“Admiral, get out of the chair.”

“You better stop and think about what you’re doing, Kirk.”

Barely containing a snarl, Khan continued to lay prone against the cold floor as Marcus spoke.

“You better think about what you did on Kronos. You made an incursion onto an enemy planet and you killed a Klingon patrol. Even if you got away without a trace, war is coming! And who is going to lead us? You? If I’m not in charge, our entire way of life is decimated! So you want me off this ship, you better kill me.”

“I will not hesitate to kill you, Sir. You threatened my crew and admitted that you had no intention of letting them live. But I would rather stun you instead, as your daughter is standing right here and I’d prefer not to kill you in front of her.”

Well, this was interesting. Kirk was more bloodthirsty than Khan had given him credit for. Khan heard the change in tone as Kirk addressed the younger Marcus.

“You alright?”

“Yes Captain.”

The difference of the sound of Kirk’s voice as his head turned to the other Marcus signaled to Khan that it was his chance. Silently, Khan stood up and jumped Kirk.

“Jim!”

Kirk attempted to fight back, and Khan lost his patience with the only person separating him from Marcus. Kirk went flying across the bridge, and Khan didn’t spare a moment to walk threateningly towards both Marcuses as the younger held her hands up in a supplicating gesture and the elder sat back in the captain’s chair, finally looking uneasy with the situation. He had not taken Kirk’s warning to heart, and for some reason, this infuriated Khan. His people were to be respected.

“Listen! Wait!”

He was done waiting, done with Starfleet, done with anyone who would keep his family from him, disrespect them, and threaten him with them. Khan threw Carol Marcus to the floor and snapped her leg, listening to her scream in agony as he advanced towards her father.

Grasping Marcus’ head in his hands, Khan had the satisfaction of watching the horror and realization dawn in his eyes as Khan began applying pressure.

“You! You should have let me sleep.”

Marcus’ skull fractured and cracked audibly, and Khan continued to press until there could be no recovery. With a final crunch that echoed around the bridge, Khan heard the last remaining Marcus scream again as she watched her father die gruesomely in front of her eyes. Khan turned towards a stunned Mr. Scott and winked. Mr. Scott dropped the phaser in his hand, and Khan walked to where Kirk was sprawled on the consoles.

Gathering up Mr. Scott’s dropped phaser, Khan pressed it to Kirk’s head. Only Khan’s was locked on stun evidently, Kirk apparently didn’t have qualms about killing after all. Khan subtly switched the phaser to stun, pressed the comm button on the console, and waited until the _Enterprise_ ’s bridge came on screen.

“I’m going to make this very simple for you.”

The Acting Captain seemed surprised, as much as a Vulcan shows emotions.

_‘Captain!’_

“Your crew for my crew.”

_‘You betrayed us.’_

“Oh, you are smart, Mr. Spock.”

Kirk’s groan signaled his return to full consciousness.

“Spock, don’t…”

Khan didn’t hesitate to smack Kirk just hard enough to knock him out again with the phaser before dropping him and addressing Commander Spock again.

“Mr. Spock, give me my crew.”

_‘And what will you do when you get them?’_

“You must have done your research by now.”

_‘Then I must refuse.’_

“Shall I destroy you, Mr. Spock? Or will you give me what I want?”

_‘We have no transporter capabilities.’_

“Fortunately, mine are perfectly functional. Drop. Your. Shields.”

_‘If I do so, I have no guarantee that you will not destroy the Enterprise.’_

Khan tilted his head and smirked at the screen.

“Well let’s play this out logically then, Mr. Spock. Firstly, I will kill your crewmates to demonstrate my resolve, then, if yours holds, I will have no choice but to kill you and your entire crew.”

_‘If you destroy our ship, you will destroy your own people.’_

“Your crew requires oxygen, mine does not. I will target your life support systems located behind the aft nacelle. And after every single person aboard you ship suffocates, I will walk over your cold corpses to recover my people. Now, shall we begin?”

Commander Spock paused a moment, no doubt weighing the truth of the statement. After a brief silence, he turned to the crew and addressed the pilot.

_‘Lower shields.’_

“A wise choice, Mr. Spock.”

Halting on the way to the scanner, Khan remembered his thought from the debris field upon crossing. In the Nerada instance, there had been a half-page report about a different ship that had come through from the supposed alternate universe. The individual had been rumored to be a Starfleet member, specifically, a Vulcan. There was only one Vulcan in Starfleet, and if the report was true, it was prudent to assume that Commander Spock and the stranger were one and the same. If that Spock was from an alternate universe that ran ahead in the timeline, it was possible Khan’s alternate self had encountered the _Enterprise_. And if that Spock had survived, it was obvious who came out the victor in that scenario.

Khan decided to test his theory.

“Mr. Spock, tell me, how is Ambassador Spock faring in this universe?”

Watching the screen closely, Khan saw the slightest widening of the eyes from Commander Spock. That cinched it. The Vulcan had a valuable resource at his disposal, and had possibly asked how Khan’s alternate self had been stopped.

_‘I am afraid I do not understand, Mr. Khan. The Vulcan ambassador is called Selek.’_

Khan was certain the Vulcan wasn’t lying, but there was still something wrong. Leaning over the console, Khan watched all seventy-two torpedoes appear on the screen out of the corner of his eye.

“I see all seventy-two torpedoes are still in their tubes. If they’re not mine, Commander, I will know it.”

Onscreen, the Vulcan tipped his head forward.

_‘Vulcans do not lie. The torpedoes are yours.’_

Again, Khan halted before beaming the torpedoes to the Vengeance. He had personally challenged the crew of the _Enterprise_ to open a torpedo before, and he was the only enemy remaining to them. Kirk’s crew had stronger morals than the man, they would not blow up seventy-two people who have done them no personal harm, but they would attempt to incapacitate or kill an enemy. Even if Vulcans did not lie, they could certainly omit. And if this Spock had really spoken to one from an alternate universe where he had been defeated by the crew of the _Enterprise_ , there was a trick here somewhere.

Khan ran a scan of the most likely places where seventy-two items could be held, and in the medbay there seemed to be many large canisters. One seemed to be separated from the rest, and Khan supposed that was Otto’s. That one was empty. Khan had attempted to mark the empty one, and he closed his scan in to the solitary figure until he could find the deep scar he had placed with a welder. It would not disable the cryotube, but it was necessary to ensure he did not leave someone behind in this next step.

“Mr. Spock, change of plan. I’m taking the cryotubes only. Are they still present in the torpedoes? Actually, I know the answer to that question. An excellent try, Acting Captain, but unfortunately, not good enough. And lying through omission is still lying.”

Onscreen, Mr. Spock seemed to deflate a little.

“I certainly hope those torpedoes are not armed. Thank you, Mr. Spock.”

Almost laughing, Khan beamed seventy-one cryotubes onboard the Vengeance. The empty one was left on the _Enterprise_ for one last use. As Khan prepared to send back the _Enterprise_ ’s crew that was still on the Vengeance, he cut the transmission with a final remark.

“Despite your attempted renegade on our deal, I will let you have your precious Kirk back. After all, no ship should go down without her Captain.”

Khan fired on the _Enterprise_ until he saw her start to list and fall. The ship was so badly damaged it wouldn’t take much to create the damage he was aiming for.

To activate Kirk’s augmented side, there would need to be a massive trauma to his system. There might also need to be a jolt to start the reaction, if Kirk had had no previous symptoms of augmentation. The cells would have adapted to disguise themselves from scanners, as had happened in the past to allow augments to infiltrate rebel human cells. 

Radiation would provide the trauma and opportunity for those augmented cells to reawaken, but Khan did not trust the _Enterprise_ ’s crew to provide proper treatment to reverse the effects, as they did not know what he knew. Khan hoped his character analysis of Kirk would hold, and that he would be the one to enter the warp core.

Security systems on the _Enterprise_ were surprisingly easy to hack with the capabilities of the Vengeance. Khan watched as Kirk and Mr. Scott ran down to engineering, changing camera views as some were hit by falling debris.

The interior of the _Enterprise_ resembled a pinwheel, and Khan observed the chaos with fascination. Mr. Scott seemed to be continuing to run his mouth in life-or-death situations, and Khan turned on the audio until he couldn’t breathe for laughter from Mr. Scott’s creative cursing.

Khan was forced to turn off the sound as debris hit the metal walls and produced some truly awful screeching sounds. The duo reached engineering, but a shift in the gravity threw both over the railing. Kirk caught himself and Mr. Scott, but appeared to be slipping. 

A young man almost materialized into view and grabbed Kirk until the gravity shifted again and they could pull themselves up. Khan was intrigued by the boy, as Mr. Scott was the Chief Engineer of the _Enterprise_ , but the boy seemed to be wearing the uniform. He wasn’t simply promoted by the easy way he acted around Kirk, and Khan recalled seeing one of the bridge crew who seemed new to the position.

As Khan continued monitoring their progress to the warp core, he became certain of his assessment of the boy. Kirk wasn’t one to suffer fools, and if this boy had been part of the bridge crew and then transferred when Mr. Scott hadn’t been around, instead of a normal engineering officer he must be quite the genius. If all went smoothly with Kirk, it may be advantageous to expand his crew further.

For now, however, it was time to bring Kirk home.

As the duo approached the warp core after the boy ran off, they paused by the console. Khan turned the sound back on to hear their conversation.

_‘Oh, no! No! No! No!’_

_‘What, Scotty?’_

_‘The housings are misaligned, there’s no way we can redirect the power!’_

Perfect.

_‘The ship is dead, sir. She’s gone.’_

_‘No she’s not.’_

Khan watched Kirk with approval as he fought to save his own crew from death. Kirk ran to the door with Mr. Scott following him, yelling.

_‘Wait, Jim! If we go in there, we’ll die. Will you listen to me? What the hell are you doing?’_

_‘I’m going in.’_

_‘That door is there to stop us from getting irradiated! We’ll be dead before we can make the climb.’_

Kirk paused for a moment before deciding.

_‘You’re not making the climb, Scotty.’_

Abruptly, Kirk whirled around and clocked his chief engineer in the jaw. Mr. Scott went down like a rock, and Kirk winced.

_‘Sorry Scotty.’_

The feed from that camera ended as Kirk dragged Mr. Scott to the console, and there were no cameras in the warp core area. Khan sighed. It was time for him to make his own preparations. Khan sent a stream of the cameras in the medbay of the _Enterprise_ to a padd, noting that the empty cryotube was still there. 

This was the riskiest part of his plan. He had to count on Kirk’s pure stubbornness to get him back out of the warp core.

He then split the screen and added a different camera from outside engineering and let the sound play from there. The door of the warp core was still visible, and he would be able to watch for Kirk if he came back out. Leaving the bridge with the padd, Khan traveled to medbay where he found a syringe and a vial. 

Only a skeleton crew had been onboard the Vengeance, and he had subdued the majority with Kirk and Mr. Scott. There were no medical personnel, and Khan prepared a biobed and filled the syringe with his blood before placing it next to the IV. When he had hacked Kirk’s file a year ago, he’d discovered they shared a blood type, which was very fortunate for Kirk. Otherwise what was about to happen would be much more complicated.

All augments could share blood for transfusion purposes, but with varying success. The chances of Kirk’s body accepting the blood if he and Khan were incompatible was very slim, and as he was not a full augment, it could kill him.

After Khan filled another syringe with his blood, he hurried back to the bridge, where he could activate the transporter beam. Of course, he could simply beam back Kirk, but he wanted his crewmates to suffer for the entirety of Starfleet for the mistreatment of Khan’s crew.

A commotion on the padd began almost as soon as he stepped back onto the bridge, in the half with the warp core area. Khan smirked as the Vulcan raced into the frame, and his smirk softened when he saw that Kirk had made it back to the door. 

The Vulcan crouched down, and Khan turned the volume up on the padd. Unfortunately, they were talking too quietly to hear, until Kirk’s hand slid down the glass and he closed his eyes. Then the Vulcan’s rage was all too loud with the volume at maximum. 

_‘KHAAAAAAAAAANNNNNNN!’_

Khan would say he was incorrect about his assertion that Vulcans could not break bones. This one looked ready for murder.

Ending the feed from that camera, Khan put the medbay feed back on the main screen. Khan saw the somber procession of crewmembers bringing Kirk to his CMO. The Vulcan had absconded back to the bridge. “Bones” sat with his head in his hands after confirming the body was Kirk. 

In the few interactions Khan had seen Kirk and his crew, it was no surprise that his death was hitting them hard. Khan stared intently at the furry ball that had been the previous recipient of his blood. It should be regaining life soon based on the likely time it had been injected, and every moment that Kirk was out of the cryotube was an increased chance of brain damage. 

Fortunately, something in the universe must have recognized that James Tiberius Kirk was not supposed to die today, and the CMO took immediate notice of the furball’s soft movement and chittering. He stared in surprise for a moment until realization crossed his face and he began yelling at his underlings.

_‘Get me that cryotube, NOW! And get the poor sod out of it, but keep them in an induced coma.’_

_'Doctor McCoy, this one is empty!'_

Another, darker, realization dawned in McCoy’s eyes.

_‘Well get Jim in there, there’s still a chance!’_

The younger Marcus caught on the fastest.

_‘How much of Khan’s blood is left?’_

_‘None.’_

Sensing the peak of the moment, and ever the drama queen, Khan chose that moment to beam over the syringe of his blood. It appeared next to the now-alive furball, and McCoy stared at the camera until Khan knew that McCoy understood he was watching. Khan was unsurprised at the hate in McCoy’s eyes, as he alone seemed to realize what Khan was doing. Later, if there was a chance, McCoy would make an excellent addition to his crew.

Carol Marcus turned to see what McCoy was staring at, and understanding blossomed as she noticed the syringe McCoy was now holding. She turned away to call the bridge as McCoy purposely blocked Kirk from view, and moments later there was an incoming hail. The Vulcan appeared on the main screen, eyes cold and filled with rage. It was fortunate that there had never been an opportunity for the Vulcan to be in reach after Kirk’s sacrifice.

_‘What are you doing?’_

Khan continued to watch the medbay feed, and after he was sure that McCoy had injected Kirk, looked back to the communication screen and smiled. In the feed, the cryotube shut with a hiss, and Khan answered the furious Vulcan onscreen as he activated the transporter.

“Why, simply recovering the last of my crew.”

Golden beams of light surrounded the cryotube containing James Kirk’s still form, and Khan was able to witness the confusion and then devastation in the Vulcan’s eyes as he processed what Khan meant. 

_‘Shields up! Mr. Sulu, put the shields up NOW!’_

“Say goodbye to your Captain, Mr. Spock.”

**Author's Note:**

> *hopefully more to come*, at least through the movie storyline.
> 
> past that, i have no idea
> 
> *i'm done! first completed work.*


End file.
